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(-) Description

Title :  STRUCTURAL CHARACTERIZATION OF A BACTERIAL 6PDH REVEALS ASPECTS OF SPECIFICITY, MECHANISM AND MODE OF INHIBITION
 
Authors :  R. Sundaramoorthy, J. Iulek, W. N. Hunter
Date :  21 Jul 06  (Deposition) - 23 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, 6-Phosphogluconate Dehydrogenase, Nadp, Pentose Shunt, Gluconate Utilization (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sundaramoorthy, J. Iulek, M. P. Barrett, O. Bidet, G. F. Ruda, I. H. Gilbert, W. N. Hunter
Crystal Structures Of A Bacterial 6- Phosphogluconate Dehydrogenase Reveal Aspects Of Specificity, Mechanism And Mode Of Inhibition By Analogues Of High-Energy Reaction Intermediates.
Febs J. V. 274 275 2007
PubMed-ID: 17222187  |  Reference-DOI: 10.1111/J.1742-4658.2006.05585.X

(-) Compounds

Molecule 1 - 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
    Chains: A
    EC Number: 1.1.1.44
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 1358
    Strain: MG1363

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
16PG1Ligand/Ion6-PHOSPHOGLUCONIC ACID
2CAC1Ligand/IonCACODYLATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
16PG2Ligand/Ion6-PHOSPHOGLUCONIC ACID
2CAC2Ligand/IonCACODYLATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:102 , SER A:128 , GLY A:129 , GLY A:130 , LYS A:184 , HIS A:187 , ASN A:188 , GLU A:191 , TYR A:192 , LYS A:262 , ARG A:289 , ILE A:367 , ARG A:447 , PHE A:450 , HIS A:453 , HOH A:2115 , HOH A:2311 , HOH A:2312 , HOH A:2313BINDING SITE FOR RESIDUE 6PG A1471
2AC2SOFTWARELYS A:262 , GLY A:451 , ALA A:452 , HIS A:453BINDING SITE FOR RESIDUE CAC A1472

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IYO)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:66 -Pro A:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IYO)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
16PGDPS00461 6-phosphogluconate dehydrogenase signature.6PGD_LACLM255-267  1A:255-267
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
16PGDPS00461 6-phosphogluconate dehydrogenase signature.6PGD_LACLM255-267  2A:255-267

(-) Exons   (0, 0)

(no "Exon" information available for 2IYO)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:470
 aligned with 6PGD_LACLM | P96789 from UniProtKB/Swiss-Prot  Length:472

    Alignment length:470
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470
           6PGD_LACLM     1 MAQANFGVVGMAVMGKNLALNVESRGYTVAIYNRTTSKTEEVYKEHQDKNLVFTKTLEEFVGSLEKPRRIMLMVQAGAATDATIKSLLPLLDIGDILIDGGNTHFPDTMRRNAELADSGINFIGTGVSGGEKGALLGPSMMPGGQKEAYDLVAPIFEQIAAKAPQDGKPCVAYMGANGAGHYVKMVHNGIEYGDMQLIAESYDLLKRILGLSNAEIQAIFEEWNEGELDSYLIEITKEVLKRKDDEGEGYIVDKILDKAGNKGTGKWTSESALDLGVPLPLITESVFARYISTYKDERVKASKVLSGPALDFSGDKKEVIEKIRKALYFSKIMSYAQGFAQLRKASEEFDWDLPYGTIAQIWRAGCIIRAEFLQNITDAFDKDSELENLLLDDYFVDITKRYQEAVRDVVSLAVQAGTPIPTFTSAISYYDSYRSENLPANLIQAQRDYFGAHTYERTDKAGIFHYDWYT 470
               SCOP domains d2iyoa1 A:1-177 automated matches                                                                                                                                                d2iyoa2 A:178-470 automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2iyoA01 A:1-181 NAD(P)-binding Rossmann-like Domain                                                                                                                                  2iyoA02 A:182-436 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                                                                    2iyoA03 A:437-470                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhh....eeee..hhhhhhhhhhhh....eee..hhhhhhhh.....eeee....hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhh..........hhhh........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..ee......ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------6PGD         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iyo A   1 MAQANFGVVGMAVMGKNLALNVESRGYTVAIYNRTTSKTEEVFKEHQDKNLVFTKTLEEFVGSLEKPRRIMLMVQAGAATDATIKSLLPLLDIGDILIDGGNTHFPDTMRRNAELADSGINFIGTGVSGGEKGALLGPSMMPGGQKEAYDLVAPIFEQIAAKAPQDGKPCVAYMGANGAGHYVKMVHNGIEYGDMQLIAESYDLLKRILGLSNAEIQAIFEEWNEGELDSYLIEITKEVLKRKDDEGEGYIVDKILDKAGNKGTGKWTSESALDLGVPLPLITESVFARYISTYKDERVKASKVLSGPALDFSGDKKEVIEKIRKALYFSKIMSYAQGFAQLRKASEEFDWDLPYGTIAQIWRAGCIIRAEFLQNITDAFDKDSELENLLLDDYFVDITKRYQEAVRDVVSLAVQAGTPIPTFTSAISYYDSYRSENLPANLIQAQRDYFGAHTYERTDKAGIFHYDWYT 470
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IYO)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (6PGD_LACLM | P96789)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004616    phosphogluconate dehydrogenase (decarboxylating) activity    Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
biological process
    GO:0019521    D-gluconate metabolic process    The chemical reactions and pathways involving D-gluconate, the anion of D-gluconic acid, the aldonic acid derived from glucose.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.

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  6PGD_LACLM | P96789
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        6PGD_LACLM | P96789: 2iyp 2iz0 2iz1

(-) Related Entries Specified in the PDB File

2iyp PRODUCT RUP
2iz0 PEX INHIBITOR-HOME DATA
2iz1 6PDH COMPLEXED WITH PEX INHIBITOR SYNCHROTRON DATA